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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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-neargene parameter #94

Closed arumds closed 4 years ago

arumds commented 4 years ago

Dear Kai,

Could you let me know what is the unit for the number given to ‘-neargene’ parameter? is it bp or kb?

I have been using ‘-neargene 2’ parameter to define variants which are 2-kb as upstream/downstream. However, all the upstream/downstream variants have dist=1. Does it mean that the argument is not parsed correctly or could it be that all the input variants are within 1-kb?

In addition how can we set the threshold for '-neargene’ as 200bp?

kaichop commented 4 years ago

The unit is base pair. So 2kb should be '-neargene 2000', rather than 'neargene 2'.